CplexA (open-source software)
“CplexA” (released on April 19th, 2010) is a Mathematica package to compute the probabilities and average properties of macromolecular assembly and its effects in gene regulation: CplexA and the tutorial are freely available at http://sourceforge.net/projects/cplexa/.
Papers that present or use results calculated using CplexA should cite:
1) The main reference for CplexA is Vilar, J.M.G. and Saiz, L. CplexA: a Mathematica package to study macromolecular- assembly control of gene expression, Bioinformatics 26, 2060-2061 (2010).
2) The biophysical background of the methods used by CplexA are described in Saiz, L. and Vilar, J.M.G. Stochastic dynamics of macromolecular-assembly networks, Mol. Syst. Biol., 2, 2006.0024 (2006).
CplexA is now available for Mathematica, Python, and Matlab. CplexA and the corresponding Mathematica, Matlab, and Python implementation tutorials are available at http://cplexa.sourceforge.net/. Software can be downloaded at http://cplexa.sourceforge.net/ tutorials are available at http://sourceforge.net/projects/cplexa/.